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  • bwa index problem - bwt file is not created

    hi,

    for some reason, i am unable to get .bwt file when executing 'bwa index' command.

    the command i am using: $ bwa index -a bwtsw filename.fa

    the fasta file, converted from fastq using fastx toolkit, is fine.
    i tried using multiple versions of bwa: 0.7.5a, 0.7.4, 0.6.1, 0.6.2, 0.5.9 but the problem persists. so i think i am doing something wrong. just can't put a pin on what.
    memory is not the issue at all as there is no indication of this in the log file (generated by the program that monitors each program).

    i have used bwa successfully in the past, so i am familiar with the program and the commands. just this time, no matter what i do, i can't get the .bwt file for post application (namely, bwa aln followed by samtools application). i am using my university's unix machines.

    any help/tips would be greatly appreciated.
    Last edited by probean; 01-20-2014, 10:02 PM.

  • #2
    Do you have write permission to the location bwa want to write the index?

    Also, bwa (at least for 0.7.5a) should autodetect which algorithm to use so -a bwtsw shouldn't be required.

    Are any of other files bwa index usually creates (eg .amb, .ann) being created?

    Comment


    • #3
      Originally posted by dcameron View Post
      Do you have write permission to the location bwa want to write the index?

      Also, bwa (at least for 0.7.5a) should autodetect which algorithm to use so -a bwtsw shouldn't be required.

      Are any of other files bwa index usually creates (eg .amb, .ann) being created?
      yes, i have permission to write. other files (.ann, .amb, .pac) are also written just fine.

      even using fresh fasta file is not helping. seems like a very odd problem i am having.

      Comment


      • #4
        If the smaller files are being written, you might want to check if you are close to any limits on either available disk space or personal or group disk quota. Bwa doesn't have the most helpful error messages when something goes wrong.

        Comment

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